1CPT | pdb_00001cpt

CRYSTAL STRUCTURE AND REFINEMENT OF CYTOCHROME P450-TERP AT 2.3 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.189 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution.

Hasemann, C.A.Ravichandran, K.G.Peterson, J.A.Deisenhofer, J.

(1994) J Mol Biology 236: 1169-1185

  • DOI: https://doi.org/10.1016/0022-2836(94)90019-1
  • Primary Citation Related Structures: 
    1CPT

  • PubMed Abstract: 

    Cytochrome P450terp is a class I (mitochondrial/bacterial) P450 that catalyzes the hydroxylation of alpha-terpineol as part of the catabolic assimilation of this compound by a pseudomonad species. Crystals grown from the purified protein have the symmetry of space group P6(1)22, and cell dimensions a = b = 69.4 A, c = 456.6 A, alpha = beta = 90 degrees, gamma = 120 degrees. Diffraction data were collected at the Cornell High Energy Synchrotron Source, and the structure of P450terp was solved by a combination of molecular replacement and multiple isomorphous replacement techniques. A model of P450terp was built and refined against native data, to an R-factor of 18.9% for data with I > or = sigma(I) between 6.0 A and 2.3 A resolution. This model contains 412 of the 428 P450terp amino acid residues; the loop between helices F and G is disordered in the crystal. While the overall fold of P450terp is very similar to that of P450cam, only three-quarters of the C alpha positions can be superimposed, to a root-mean-square deviation of only 1.87 A. The mode of substrate binding by P450terp can be predicted, and probable substrate contact residues identified. The heme environment and side-chain positions in the adjacent I-helix suggest possible modes of proton delivery in the catalytic cycle of the enzyme.


  • Organizational Affiliation
    • Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050.

Macromolecule Content 

  • Total Structure Weight: 48.59 kDa 
  • Atom Count: 3,521 
  • Modeled Residue Count: 412 
  • Deposited Residue Count: 428 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CYTOCHROME P450-TERP428Pseudomonas sp.Mutation(s): 0 
EC: 1.14
UniProt
Find proteins for P33006 (Pseudomonas sp)
Explore P33006 
Go to UniProtKB:  P33006
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33006
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.189 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.44α = 90
b = 69.44β = 90
c = 456.55γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other